fsl cluster
#!/bin/sh
# The following examples are used for evaluating binary manual lesion masks
# to identify freckles that should be removed.
# Define the connectivity number in terms of
# the way the voxels touch each other (faces, edges, corners):
# 6 is harshest criterion (only touching faces count as connected),
# 18 is next (touching faces or edges count),
# 26 is the most lenient connectivity criterion
# (touching faces, edges, or corners count)
# List cluster sizes at the designated connectivity
cluster -i img -t 1 --connectivity=${number}
# Create a temporary image (img_cluster_size) with a connectivity of ${number}"
cluster -i img -t 1 --connectivity=${number} --no_table --osize=img_cluster_size
# Threshold the temporary image and name the output=the original input image
# Note the output data type assumes this is a binary mask.
fslmaths img_cluster_size -thr ${thresh} -bin img -odt char